This is a 371 of PCT/GB98/01714, filed Jun. 12, 1998, which claims priority from GB 9712415.0, filed Jun. 13, 1997.
This invention relates to the genetic control of flowering in plants and the cloning and expression of genes involved therein. More particularly, the invention relates to the cloning and expression of the EARLY SHORT DAYS 4 gene of Arabidopsis thaliana, and homologues from other species, and manipulation and use of these genes in plants.
Efficient flowering in plants is important, particularly when the intended product is the flower or the seed produced therefrom. One aspect of this is the timing of flowering: advancing or retarding the onset of flowering can be useful to farmers and seed producers. An understanding of the genetic mechanisms which influence flowering provides a means for altering the flowering characteristics of the target plant. Species for which flowering is important to crop production are numerous, essentially all crops which are grown from seed, with important examples being the cereals, rice and maize, probably the most agronomically important in warmer climatic zones, and wheat, barley, oats and rye in more temperate climates. Important seed products are oil seed rape and canola, sugar beet, maize, sunflower, soybean and sorghum. Many crops which are harvested for their roots or leaves are, of course, grown annually from seed and the production of seed of any kind is very dependent upon the ability of the plant to flower, to be pollinated and to set seed. Delaying flowering is important in increasing the yield of plants from which the roots or leaves are harvested. In horticulture, control of the timing of flowering is important. Horticultural plants whose flowering may be controlled include lettuce, endive, spinach and vegetable brassicas including cabbage, broccoli and cauliflower, and carnations and geraniums.
Arabidopsis thaliana is a facultative long day plant, flowering early under long days and late under short days. Because it has a small, well-characterized genome, is relatively easily transformed and regenerated and has a rapid growing cycle, Arabidopsis is an ideal model plant in which to study flowering and its control.
The present inventors have discovered that one of the genes that regulates flowering time in Arabidopsis is a gene termed the EARLY SHORT DAYS 4 or ESD4 gene. The present inventors have found that plants carrying a recessive mutation affecting the ESD4 gene flower earlier than their wild-types under long and short days. The ESD4 gene has now been cloned and sequenced and the inventors have demonstrated that the mutation is a deletion removing part of the gene. This provides indication that reducing or abolishing ESD4 function accelerates flowering, and therefore that the ESD4 gene likely encodes a repressor of flowering.
According to a first aspect of the present invention there is provided a nucleic acid molecule including a nucleotide sequence encoding a polypentide with ESD4 function. Those skilled in the art will appreciate that xe2x80x9cESD4 functionxe2x80x9d may be used to refer to the ability to influence the timing, of flowering phenotypically when its expression is reduced like the ESD4 gene of Arabidopsis thaliana. esd4 mutants exhibit early flowering under long and short days, the timing of flowering being substantially unaffected by vernalisation.
The present invention provides a nucleic acid isolate encoding a polypeptide including the amino acid sequence shown in FIG. 1, which may include the coding sequence shown in FIG. 1 which is that of the ESD4 gene of Arabidopsis thaliana. FIG. 2 shows a genomic sequence including nucleotides encoding the polypeptide for which the amino acid sequence is shown in FIG. 1.
Nucleic acid according to the present invention may have the sequence of an ESD4 gene of Arabidopsis thaliana, or be a mutant, variant, derivative or allele or a homologue of the sequence provided. Preferred mutants, variants, derivatives and alleles are those which encode a protein which retains a functional characteristic of the protein encoded by the wild-type gene, especially the ability to affect a physical characteristic of a plant, such as a flowering characteristic, especially the ability to repress flowering as discussed herein.
A mutant, variant, derivative or allele in accordance with the present invention may have the ability to affect a physical characteristic of a plant, particularly a flowering characteristic. In various embodiments a mutant, variant, derivative or allele represses flowering compared with wild-type on expression in a plant, e.g. compared with the effect obtained using a gene sequence encoding the polypeptide of FIG. 1. xe2x80x9cRepressionxe2x80x9d of flowering delays, retards, inhibits or slows it down. In other embodiments, a mutant, variant, derivative or allele promotes flowering compared with wild-type on expression in a plant, e.g. compared with the effect obtained using a gene sequence encoding the polypeptide of FIG. 1. xe2x80x9cPromotionxe2x80x9d of flowering advances, accelerates or brings it forward. Comparison of effect on flowering or other characteristic may be performed in Arabidopsis thaliana, although nucleic acid according to the present invention may be used in the production of a wide variety of plants and for influencing a characteristic thereof.
As discussed further below, over-expression of nucleic acid according to the present invention may delay flowering while under expression may promote flowering in a transgenic plant.
Changes to a sequence, to produce a mutant, variant or derivative, may be by one or more of addition, insertion, deletion or substitution of one or more nucleotides in the nucleic acid, leading to the addition, insertion, deletion or substitution of one or more amino acids in the encoded polypeptide. Of course, changes to the nucleic acid which make no difference to the encoded amino acid sequence are included.
A preferred nucleic acid sequence for an ESD4 gene including a coding sequence according to the present invention is shown in FIG. 1, along with the predicted amino acid sequence of a polypeptide according to the present invention which has ESD4 function.
A mutant, allele, variant or derivative amino acid sequence in accordance with the present invention may include within the sequence shown in FIG. 1, a single amino acid change with respect to the sequence shown in FIG. 1, or 2, 3, 4, 5, 6, 7, 8, or 9 changes, about 10, 15, 20, 30, 40 or 50 changes, or greater than about 50, 60, 70, 80 or 90 changes. In addition to one or more changes within the amino acid sequence shown in FIG. 1, a mutant, allele, variant or derivative amino acid sequence may include additional amino acids at the C-terminus and/or N-terminus.
A sequence related to a sequence specifically disclosed herein shares homology with that sequence. Homology may be at the nucleotide sequence and/or amino acid sequence level. Preferably, the nucleic acid and/or amino acid sequence shares homology with the coding sequence or the sequence encoded by the nucleotide sequence of FIG. 1, preferably at least about 50%, or 60%, or 70%, or 80% homology, most preferably at least about 90%, 95%, 96%, 97%, 98% or 99% homology.
As is well-understood, homology at the amino acid level is generally in terms of amino acid similarity or identity. Similarity allows for xe2x80x9cconservative variationxe2x80x9d, i.e. substitution of one hydrophobic residue such as isoleucine, valine, leucine or methionine for another, or the substitution of one polar residue for another, such as arginine for lysine, glutamic for aspartic acid, or glutamine for asparagine. Similarity may be as defined and determined by the TBLASTN program, of Altschul et al. (1990) J. Mol. Biol. 215: 403-10, which is in standard use in the art, or, and this may be preferred, the standard program BestFit, which is part of the Wisconsin Package, Version 8, September 1994, (Genetics Computer Group, 575 Science Drive, Madison, Wisconsin, USA, Wisconsin 53711). BestFit makes an optimal alignment of the best segment of similarity between two sequences. Optimal alignments are found by inserting gaps to maximize the number of matches using the local homology algorithm of Smith and Waterman (Adv. Appl. Math. (1981) 2: 482-489).
Homology may be over the full-length of the relevant sequence shown herein, or may more preferably be over a contiguous sequence of about or greater than about 20, 25, 30, 33, 40, 50, 67, 133, 167, 200, 233, 267, 300, 333 or more amino acids or codons, compared with the relevant amino acid sequence or nucleotide sequence as the case may be.
Also provided by an aspect of the present invention is nucleic acid including or consisting essentially of a sequence of nucleotides complementary to a nucleotide sequence hybridisable with any encoding sequence provided herein. Another way of looking at this would be for nucleic acid according to this aspect to be hybridisable with a nucleotide sequence complementary to any encoding sequence provided herein. Of course, DNA is generally double-stranded and blotting techniques such as Southern hybridisation are often performed following separation of the strands without a distinction being drawn between which of the strands is hybridising. Preferably the hybridisable nucleic acid or its complement encode a product able to influence a physical characteristic of a plant, particularly a flowering characteristic such as the timing of flowering. Preferred conditions for hybridisation are familiar to those skilled in the art, but are generally stringent enough for there to be positive hybridisation between the sequences of interest to the exclusion of other sequences.
The nucleic acid, which may contain for example DNA encoding the amino acid sequence of FIG. 1, as genomic (see e.g. FIG. 2) or cDNA, may be in the form of a recombinant and preferably replicable vector, for example a plasmid, cosmid, phage or Agrobacterium binary vector. The nucleic acid may be under the control of an appropriate promoter or other regulatory elements for expression in a host cell such as a microbial, e.g. bacterial, or plant cell. In the case of genomic DNA, this may contain its own promoter or other regulatory elements and in the case of cDNA this may be under the control of an appropriate promoter or other regulatory elements for expression in the host cell.
A vector including nucleic acid according to the present invention need not include a promoter or other regulatory sequence, particularly if the vector is to be used to introduce the nucleic acid into cells for recombination into the genome.
Those skilled in the art are well able to construct vectors and design protocols for recombinant gene expression. Suitable vectors can be chosen or constructed, containing appropriate regulatory sequences, including promoter sequences, terminator fragments, polyadenylation sequences, enhancer sequences, marker genes and other sequences as appropriate. For further details see, for example, Molecular Cloning: a Laboratory Manual: 2nd edition, Sambrook et al, 1989, Cold Spring Harbor Laboratory Press. Many known techniques and protocols for manipulation of nucleic acid, for example in preparation of nucleic acid constructs, mutagenesis, sequencing, introduction of DNA into cells and gene expression, and analysis of proteins, are described in detail in Current Protocols in Molecular Biology, Second Edition, Ausubel et al. eds., John Wiley and Sons, 1992. The disclosures of Sambrook et al. and Ausubel et al. are incorporated herein by reference. Specific procedures and vectors previously used with wide success upon plants are described by Bevan (Nucl. Acids Res. 12, 8711-8721 (1984)) and Guerineau and Mullineaux (1993) (Plant transformation and expression vectors. In: Plant Molecular Biology Labfax (Croy RRD ed) Oxford, BIOS Scientific Publishers, pp 121-148).
Selectable genetic markers may be used consisting of chimaeric genes that confer selectable phenotypes such as resistance to antibiotics such as kanamycin, hygromycin, phosphinotricin, chlorsulfuron, methotrexate, gentamycin, spectinomycin, imidazolinones and glyphosate.
Nucleic acid molecules and vectors according to the present invention may be provided isolated and/or purified from their natural environment, in substantially pure or homogeneous form, or free or substantially free of nucleic acid or genes of the species of interest or origin other than the sequence encoding a polypeptide with the required function. Nucleic acid according to the present invention may include cDNA, RNA, genomic DNA and may be wholly or partially synthetic. The term xe2x80x9cisolatexe2x80x9d encompasses all these possibilities. Where a DNA sequence is specified, e.g. with reference to a figure, unless context requires otherwise the RNA equivalent, with U substituted for T where it occurs, is encompassed.
When introducing a chosen gene construct into a cell, certain considerations must be taken into account, well known to those skilled in the art. The nucleic acid to be inserted should be assembled within a construct which contains effective regulatory elements which will drive transcription. There must be available a method of transporting the construct into the cell. Once the construct is within the cell membrane, integration into the endogenous chromosomal material either will or will not occur. Finally, as far as plants are concerned the target cell type must be such that cells can be regenerated into whole plants.
Plants transformed with the DNA segment containing the sequence may be produced by standard techniques which are already known for the genetic manipulation of plants. DNA can be transformed into plant cells using any suitable technology, such as a disarmed Ti-plasmid vector carried by Agrobacterium exploiting its natural gene transfer ability (EP-A-270355, EP-A-0116718, NAR 12(22) 8711-87215 1984), particle or microprojectile bombardment (US 5100792, EP-A-444882, EP-A-434616) microinjection (WO 92/09696, WO 94/00583, EP 331083, EP 175966, Green et al. (1987) Plant Tissue and Cell Culture, Academic Press), electroporation (EP 290395, WO 8706614 Gelvin Debeyserxe2x80x94see attached) other forms of direct DNA uptake (DE 4005152, WO 9012096, US 4684611), liposome mediated DNA uptake (e.g. Freeman et al.
Plant Cell Physiol. 29: 1353 (1984)) or the vortexing method (e.g. Kindle, PNAS U.S.A. 87: 1228 (1990d) Physical methods for the transformation of plant cells are reviewed in Oard, 1991, Biotech. Adv. 9: 1-11.
Agrobacterium transformation is widely used by those skilled in the art to transform dicotyledonous species. Recently, there has been substantial progress towards the routine production of stable, fertile transgenic plants in almost all economically relevant monocot plants (criyama, et al. (1988) Bio/Technology 6, 1072-1074; Zhang, et al. (1988) Plant Cell Rep. 7, 379-384; Zhang, et al. (1988) Theor Appl Genet 76, 835-840; Shimamoto, et al. (1989) Nature 338, 274-276; Datta, et al. (1990) Bio/Technology 8, 736-740; Christou, et al. (1991) Bio/Technology 9, 957-962; Peng, et al. (1991) International Rice Research Institute, Manila, Philippines 563-574; Cao, et al. (1992) Plant Cell Rep. 11, 585-591; Li, et al. (1993) Plant Cell Rep. 12, 250-255; Rathore, et al. (1993) Plant Molecular Biology 21, 871-884; Fromm, et al. (1990) Bio/Technology 8, 833-839; Gordon-Kamm, et al. (1990). Plant Cell 2, 603-618; D""Halluin, et al. (1992) Plant Cell 4, 1495-1505; Walters, et al. (1992) Plant Molecular Biology 18, 189-200; Koziel, et al. (1993) Biotechnology 11, 194-200; Vasil, I. K. (1994) Plant Molecular Biology 25, 925-937; Weeks, et al. (1993) Plant Physiology 102, 1077-1084; Somers, et al. (1992), Bio/Technology 10, 1589-1594; WO92/14828). In particular, Agrobacterium mediated transformation is now emerging also as an highly efficient alternative transformation method in monocots (Hiei et al. (1994) The Plant Journal 6, 271-282)
The generation of fertile transgenic plants has been achieved in the cereals rice, maize, wheat, oat, and barley (reviewed in Shimamoto, K. (1994) Current Opinion in Biotechnology 5, 158-162.; Vasil, et al. (1992) Bio/Technology 10, 667-674; Vain et al., 1995, Biotechnology Advances 13 (4): 653-671; Vasil, 1996, Nature Biotechnology 14 page 702).
Microprojectile bombardment, electroporation and direct DNA uptake are preferred where Agrobacterium is inefficient or ineffective. Alternatively, a combination of different techniques may be employed to enhance the efficiency of the transformation process, eg bombardment with Agrobacterium coated microparticles (EP-A-486234) or microprojectile bombardment to induce wounding followed by co-cultivation with Agrobacterium (EP-A-486233).
Following transformation, a plant may be regenerated, e.g. from single cells, callus tissue or leaf discs, as is standard in the art. Almost any plant can be entirely regenerated from cells, tissues and organs of the plant. Available techniques are reviewd in Vasil et al., Cell Culture and Somatic Cell Genetics of Plants, Vol I, II and III, Laboratory Procedures and Their Applications, Academic Press, 1984, and Weissbach and Weissbach, Methods for Plant Molecular Biology; Academic Press, 1989.
The particular choice of a transformation technology will be determined by its efficiency to transform certain plant species as well as the experience and preference of the person practising the invention with a particular methodology of choice. It will be apparent to the skilled person that the particular choice of a transformation system to introduce nucleic acid into plant cells is not essential to or a limitation of the invention, nor is the choice of technique for plant regeneration.
A ESD4 gene and modified versions thereof (alleles, mutants, variants and derivatives thereof), and other nucleic acid provided herein, including species homologues, may be used to affect a physical characteristic, such as a flowering characteristic which may include timing of flowering, in plants. For this purpose nucleic acid such as a vector as described herein may be used for the production of a transgenic plant. Such a plant may possess an altered flowering phenotype, particular in terms of timing of flowering, compared with wild-type (that is to say a plant that is wild-type for ESD4 or the relevant homologue thereof).
The invention further encompasses a host cell transformed with nucleic acid or a vector according tot he present invention, especially a plant or a microbial cell. Thus, a host cell, such as a plant cell, including heterologous nucleic acid according to the present invention is provided. Within the cell, the nucleic acid may be incorporated within the chromosome. There may be more than one heterologous nucleotide sequence per haploid genome.
Also according to the invention there is provided a plant cell having incorporated into its genome nucleic acid, particularly heterologous nucleic acid, as provided by the present invention, under operative control of a regulatory sequence for control of expression. The coding sequence may be operably linked to one or more regulatory sequences which may be heterologous or foreign to the gene, such as not naturally associated with the gene for its expression. The nucleic acid according to the invention may be placed under the control of an externally inducible gene promoter to place expression under the control of the user.
A suitable inducible promoter is the GST-II-27 gene promoter which has been shown to be induced by certain chemical compounds which can be applied to growing plants. The promoter is functional in both monocotyledons and dicotyledons. It can therefore be used to control gene expression in a variety of genetically modified plants, including field crops such as canola, sunflower, tobacco, sugarbeet, cotton; cereals such as wheat, barley, rice, maize, sorghum; fruit such as tomatoes, mangoes, peaches, apples, pears, strawberries, bananas, and melons; and vegetables such as carrot, lettuce, cabbage and onion. The GST-II-27 promoter is also suitable for use in a variety of tissues, including roots, leaves, stems and reproductive tissues. Another example of an inducible promoter is the ethanol inducible gene switch disclosed in Caddick et al (1998) Nature Biotechnology 16: 177-180. Many other examples are known to those skilled in the art.
Other suitable promoters may include the Cauliflower Mosaic Virus 35S (CaMV 35S) gene promoter that is expressed at a high level in virtually all plant tissues (Benfey et al, (1990a) EMBO J 9: 1677-1684); the cauliflower meri 5 promoter that is expressed in the vegetative apical meristem as well as several well localised positions in the plant body, eg inner phloem, flower primordia, branching points in root and shoot (Medford, J. I. (1992). Plant Cell 4, 1029-1039; Medford et al, (1991) Plant Cell 3, 359-370) and the Arabidorsis thaliana LEAFY promoter that is expressed very early in flower development (Weigel et al, (1992) Cell 69, 843-859).
A further aspect of the present invention provides a method of making such a plant cell involving introduction of nucleic acid or a suitable vector including the sequence of nucleotides into a plant cell and causing or allowing recombination between the vector and the plant cell genome to introduce the sequence of nucleotides into the genome. The invention extends to plant cells containing nucleic acid according to the invention as a result of introduction of the nucleic acid into an ancestor cell.
The term xe2x80x9cheterologousxe2x80x9d may be used to indicate that the gene/sequence of nucleotides in question have been introduced into said cells of the plant or an ancestor thereof, using genetic engineering, ie by human intervention. A transgenic plant cell, i.e. transgenic for the nucleic acid in question, may be provided. The transgene may be on an extra-genomic vector or incorporated, preferably stably, into the genome. A heterologous gene may replace an endogenous equivalent gene; ie one which normally performs the same or a similar function, or the inserted sequence may be additional to the endogenous gene or other sequence. An advantage of introduction of a heterologous gene is the ability to place expression of a sequence under the control of a promoter of choice, in order to be able to influence expression according to preference. Furthermore, mutants, variants and derivatives of the wild-type gene, e.g. with higher or lower activity than wild-type, may be used in place of the endogenous gene. Nucleic acid heterologous, or exogenous or foreign, to a plant cell may be non-naturally occuring in cells of that type, variety or species. Thus, nucleic acid may include a coding sequence of or derived from a particular type of plant cell or species or variety of plant, placed within the context of a plant cell of a different type or species or variety of plant. A further possibility is for a nucleic acid sequence to be placed within a cell in which it or a homologue is found naturally, but wherein the nucleic acid sequence is linked and/or adjacent to nucleic acid which does not occur naturally within the cell, or cells of that type or species or variety of plant, such as operably linked to one or more regulatory sequences, such as a promoter sequence, for control of expression. A sequence within a plant or other host cell may be identifiably heterologous, exogenous or foreign.
Plants which include a plant cell according to the invention are also provided, along with any part or propagule thereof, seed, selfed or hybrid progeny and descendants. A plant according to the present invention may be one which does not breed true in one or more properties. Plant varieties may be excluded, particularly registrable plant varieties according to Plant Breeders"" Rights. It is noted that a plant need not be considered a xe2x80x9cplant varietyxe2x80x9d simply because it contains stably within its genome a transgene, introduced into a cell of the plant or an ancestor thereof.
In addition to a plant, the present invention provides any clone of such a plant, seed, selfed or hybrid progeny and descendants, and any part of any of these, such as cuttings, seed. The invention provides any plant propagule, that is any part which may be used in reproduction or propagation, sexual or asexual, including cuttings, seed and so on. Also encompassed by the invention is a plant which is a sexually or asexually propagated off-spring, clone or descendant of such a plant, or any part or propagule of said plant, off-spring, clone or descendant.
The invention further provides a method of influencing or affecting a physical e.g. flowering characteristic such as the timing of flowering of a plant, including causing or allowing expression of a heterologous nucleic acid sequence as discussed within cells of the plant.
The invention further provides a method of including expression from nucleic acid encoding the amino acid sequence of FIG. 1, or a mutant, variant, allele or derivative of the sequence, within cells of a plant (thereby producing the encoded polypeptide), following an earlier step of introduction of the nucleic acid into a cell of the plant or an ancestor thereof. Such a method may influence or affect a flowering characteristic of the plant, such as the timing of flowering. This may be used in combination with any other gene, such as transgenes involved in flowering or other phenotypic trait or desirable property.
The present invention also encompasses the expression product of any of the nucleic acid sequences disclosed and methods of making the expression product by expression from encoding nucleic acid therefore under suitable conditions, which may be in suitable host cells. Following expression, the product may be isolated from the expression system and may be used as desired, for instance in formulation of a composition including at least one additional component.
A further aspect of the present invention provides a method of identifying and cloning ESD4 homologues from plant species other than Arabidopsis thaliana which method employs a nucleotide sequence derived from that shown in FIG. 1. Sequences derived from these may themselves be used in identifying and in cloning other sequences. The nucleotide sequence information provided herein, or any part thereof, may be used in a data-base search to find homologous sequences, expression products of which can be tested for ability to influence a flowering characteristic. These may have ESD4 function or the ability to repress flowering. Alternatively, nucleic acid libraries may be screened using techniques well known to those skilled in the art and homologous sequences thereby identified then tested.
Target or candidate nucleic acid may, for example, comprise genomic DNA, cDNA or RNA (or a mixture of any of these preferably as a library) obtainable from an organism known to contain or suspected of containing such nucleic acid, either monocotyledonous or dicotyledonous. Prior to any PCR that is to be performed, the complexity of a nucleic acid library may be reduced by creating a cDNA library for example using RT-PCR or by using the phenol emulsion reassociation technique (Clarke et al. (1992) NAR 20, 1289-1292) on a genomic library. Successful hybridisation may be identified and target/candidate nucleic acid isolated for further investigation and/or use.
Hybridisation of nucleic acid molecule to a ESD4 gene or homologue may be determined or identified indirectly, e.g using a nucleic acid amplification reaction, particularly the polymerase chain reaction (PCR). PCR requires theuse of two primers to specifically amplify target nucleic acid, so preferably two nucleic acid molecules with sequences characteristic of ESD4 are employed. However, if RACE is used, only one such primer may be needed. Hybridisation may be also be determined (optionally in conjunction with an amplification technique such as PCR) by probing with nucleic acid and identifying positive hybridisation under suitably stringent conditions (in accordance with known techniques). For probing, preferred conditions are those which are stringent enough for there to be a simple pattern with a small number of hybridisations identified as positive which can be investigated further. It is well known in the art to increase stringency of hybridisation gradually until only a few positive clones remain.
Binding of a probe to target nucleic acid (e.g. DNA) may be measured using any of a variety of techniques at the disposal of those skilled in the art. For instance, probes may be radioactively, fluorescently or enzymatically labelled. Other methods not employing labelling of probe include examination of restriction fragment length polymorphisms, amplification using PCR, RNAase cleavage and allele specific oligonucleotide probing.
Probing may employ the standard Southern blotting technique. For instance DNA may be extracted from cells and digested with different restriction enzymes. Restriction fragments may then be separated by electrophoresis on an agarose gel, before denaturation and transfer to a nitrocellulose filter. Labelled probe may be hybridised to the DNA fragments on the filter and binding determined. DNA for probing may be prepared from RNA preparations from cells by techniques such as reverse-transcriptase- PRC.
Preliminary experiments may be performed by hybridising under low stringency conditions various probes to Southern blots of DNA digested with restriction enzymes. For probing, preferred conditions are those which are stringent enough for there to be a simple pattern with a small number ofhybridisations identified as positive which can be investigated further. It is well known in the art to increase stringency of hybridisation gradually until only a few positive clones remain. Suitable conditions would be achieved when a large number of hybridising fragments were obtained while the background hybridisation was low. Using these conditions nucleic acid libraries, e.g. cDNA libraries representative of expressed sequences, may be searched. Those skilled in the art are well able to employ suitable conditions of the desired stringency for selective hybridisation, taking into account factors such as oligonucleotide length and base composition, temperature and so on.
For instance, screening may initially be carried out under conditions, which comprise a temperature of about 37xc2x0 C. or more, a formamide concentration of less than about 50%, and a moderate to low salt (e.g. Standard Saline Citrate (xe2x80x98SSCxe2x80x99)=0.15 M sodium chloride; 0.15 M sodium citrate; pH 7) concentration.
Alternatively, a temperature of about 50xc2x0 C. or more and a high salt (e.g. xe2x80x98SSPExe2x80x99=0.180 mM sodium chloride; 9 mM disodium hydrogen phosphate; 9 mM sodium dihydrogen phosphate; 1 mM sodium EDTA; pH 7.4). Preferably the screening is carried out at about 37xc2x0 C., a formamide concentration of about 20%, and a salt concentration of about 5xc3x97SSC, or a temperature of about 50xc2x0 C. and a salt concentration of about 2xc3x97SSPE. These conditions will allow the identification of sequences which have a substantial degree of homology (similarity, identity) with the probe sequence, without requiring the perfect homology for the identification of a stable hybrid.
Suitable conditions include, e.g. for detection of sequences that are about 80-90% identical, hybridization overnight at 42xc2x0 C. in 0.25M Na2HPO4, pH 7.2, 6.5% SDS, 10% dextran sulfate and a final wash at 55xc2x0 C. in 0.1xc3x97SSC, 0.1% SDS. For detection of sequences that are greater than about 90%, identical, suitable conditions include hybridization overnight at 65xc2x0 C. in 0.25M Na2HPO4, pH 7.2, 6.50% SDS, 10% dextran sulfate and a final wash at 60xc2x0 C. in 0.1xc3x97SSC, 0.1% SDS.
PCR techniques for the amplification of nucleic acid are described in U.S. Pat. No. 4,683,195 and Saiki et al. Science 239: 487-491 (1988). PCR includes steps of denaturation of template nucleic acid (if double-stranded), annealing of primer to target, and polymerisation. The nucleic acid probed or used as template in the amplification reaction may be genomic DNA, cDNA or RNA. PCR may be used to amplify specific sequences from genomic DNA, specific RNA sequences and cDNA transcribed from mRNA. References for the general use of PCR techniques include Mullis et al, Cold Spring Harbor Symp. Quant. Biol., 51:263, (1987), Ehrlich (ed), PCR technology, Stockton Press, NY, 1989, Ehrlich et al, Science, 252:1643-1650, (1991), xe2x80x9cPCR protocols; A Guide to Methods and Applicationsxe2x80x9d, Eds. Innis et al, Academic Press, New York, (1990).
Assessment of whether or not a PCR product corresponds to a gene able to alter a plant""s characteristics, particularly a flowering characteristic, may be conducted in various ways, as discussed, and a PCR band may contain a complex mix of products. Individual products may be cloned and each screened for linkage to such known genes that are segregating in progeny that showed a polymorphism for this probe. Alternatively, the PCR product may be treated in a way that enables one to display the polymorphism on a denaturing polyacrylamide DNA sequencing gel with specific bands that are linked to the gene being preselected prior to cloning. Once a candidate PCR band has been cloned and shown to be linked to a known flowering gene, it may be used to isolate clones which may be inspected for other features and homologies to ESD4/ESD4 or other related gene. It may subsequently be analysed by transformation to assess its function on introduction into a plant of interest. Alternatively, the PCR band or sequences derived by analysing it may be used to assist plant breeders in monitoring the segregation of a useful gene.
Preferred amino acid sequences suitable for use in the design of probes or PCR primers are sequences conserved (completely, substantially or partly) between at least two ESD4 peptides or polypeptides encoded by genes involved in control of flowering in a plant. Conserved nucleotide sequences may be identified from the nucleotide sequence information contained herein.
On the basis of amino acid sequence information or nucleotide sequence information, oligonucleotide probes or primers may be designed (when working from amino acid sequence information, taking into account the degeneracy of the genetic code and where appropriate, codon usage of the organism).
A gene or fragment thereof identified as being that to which a said nucleic acid molecule hybridises, which may be an amplified PCR may be isolated and/or purified and may be subsequently investigated for ability to alter a flowering characteristic of a plant. If the identified nucleic acid is a fragment of a gene, the fragment may be used (e.g. by probing and/or PCR) in subsequent cloning of the full-length gene, which may be a full-length coding sequence. Inserts may be prepared from partial cDNA clones and used to screen cDNA libraries. The full-length clones isolated may be subcloned into expression vectors and activity assayed by introduction into suitable host cells and/or sequenced. It may be necessary for one or more gene fragments to be ligated to generate a full-length coding sequence.
Molecules found to manipulate genes with ability to alter a plant""s flowering characteristics may be used as such, i.e. to alter a flowering characteristic of a plant. Nucleic acid obtained and obtainable using a method as disclosed herein is provided in various aspects of the present inventions.
The present application also provides oligonucleotides based on either an ESD4 nucleotide sequence as provided herein or an ESD4, nucleotide sequence obtainable in accordance with the disclosures and suggestions hereon. The oligonucleotides may be of a length suitable for use as primers in an amplification reaction, or they may be suitable for use as hybridization fishing probes. Preferably an oligonucleotide in accordance with the invention, e.g. for use in nucleic acid amplification, has about 10 or fewer codons (e.g. 6, 7 or 8), i.e. is about 30 or fewer nucleotides in length (e.g. 18, 21 or 24).
The present invention also extends to nucleic acid encoding an ESD4 homologue obtained using a nucleotide sequence derived from that shown in FIG. 1.
The ESD4 gene has a novel sequence. No Arabidopsis genes showing significant homology to ESD4 were identified in public database. However, a region of the ESD4 protein showed homology to Expressed Sequence Tags (ESTs) of unknown function isolated from rice and mammals (FIG. 3) (SEQ ID NO:27).
In certain embodiments, nucleic acid according to the present invention encodes a polypeptide which has homology with all or part of the amino acid sequence shown in FIG. 1, in the terms discussed already above (e.g. for length) which homology is greater over the length of the relevant part (i.e. fragment) than the homology shared between a respective part of the amino acid sequence of FIG. 1 and the EST sequences shown in FIG. 3, and may be greater than about 5% greater, more preferably greater than about 10% greater, more preferably greater than about 20% greater, and more preferably greater than about 30% greater. Thus, to exemplify with reference to one embodiment, nucleic acid encoding an amino acid mutant, variant or derivative of the amino acid sequence shown in FIG. 1 may be provided wherein the encoded amino acid sequence includes a contiguous sequence of about 100 amino acids which has greater homology with a contiguous sequence of 100 amino acids within the amino acid sequence of FIG. 1 than any contiguous sequence of 100 amino acids within an EST sequence such as shown in FIG. 5, preferably greater than about 5% greater homology, and so on.
Similarly, nucleic acid according to certain embodiments of the present invention may have homology with all or part of the nucleotide sequence shown in FIG. 1 or FIG. 2, in the terms discussed already above (e.g. for length), which homology is greater over the length of the relevant part (i.e. fragment) than the homology shared between a respective part of the nucleotide sequence of FIG. 1 or FIG. 2 and FIG. 4A or FIG. 4B and may be greater than about 5% greater, more preferably greater than about 10% greater, more preferably greater than about 20% greater, and more preferably greater than about 30% greater. Thus, to exemplify with reference to one embodiment, nucleic acid may be provided in accordance with the present invention wherein the nucleotide sequence includes a contiguous sequence of about 300 nucleotides (or 100 codons) which has greater homology with a contiguous sequence of 300 nucleotides within the nucleotide sequence of FIG. 1 or FIG. 2 than any contiguous sequence of 100 nucleotides within an EST sequence such as shown in FIG. 4A or FIG. 4B, preferably greater than about 5% greater homology, and so on.
The provision of sequence information for the ESD4 gene of Arabidopsis thaliana enables the obtention of homologous sequences from other plant species. In particular, it should be possible to easily isolate ESD4 homologues from related, commercially important Brassica species (e.g. Brassica nigra, Brassica napus and Brassica oleraceae), as has been done for other flowering time genes isolated from Arabidopsis (e.g CO; WO 96/14414).
Thus, included within the scope of the present invention are nucleic acid molecules which encode amino acid sequences which are homologues of ESD4 of Arabidopsis thaliana. Homology may be at the nucleotide sequence and/or amino acid sequence level, as has already been discussed above. A homologue from a species other than Arabidopsis thaliana encodes a product which causes a phenotype similar to that caused by the Arabidopsis thaliana ESD4 gene, generally including the ability to influence a flowering characteristic such as the timing of flowering. In addition, mutants, derivatives or alleles of these genes may promote or delay flowering compared with wild-type. ESD4 gene homologues may also be identified from economically important monocotyledonous crop plants such as rice and maize. Although genes encoding the same protein in monocotyledonous and dicotyledonous plants show relatively little homology at the nucleotide level, amino acid sequences are conserved. Therefore it is possible to use public sequence databases to identify Arabidopsis, rice or maize cDNA clone sequences that were obtained in random sequencing programmes and share homology to the gene of interest, as has been done for other flowering time genes isolated from Arabidopsis (e.g CO; WO 96/14414). A gene related to ESD4 has been isolated from rice as an expressed sequence tag (FIG. 3). Of course, mutants, derivatives and alleles of these sequences are included within the scope of the present invention in the same terms as discussed above for the Arabidopsis thaliana ESD4 gene.
Nucleic acid according to the invention may include a nucleotide sequence encoding a product whose wild-type function is to repress flowering. Reducing the level of expression, as in the esd4 mutant, may be used to accelerate flowering, while increasing the level of expression may be used to delay flowering. The ESD4 gene product is an active repressor of flowering, while genes such as CO and LD encode proteins that promote flowering. The over-expression of the LHY gene delays flowering.
The principal physical characteristic, actually a flowering characteristic, which may be altered using the present invention is the timing of flowering. Reduction in expression of the gene product of the ESD4 gene may be used to promote early flowering (in accordance with the esd4 mutant phenotype), and over-expression may be used to delay flowering. This degree of control is useful to ensure synchronous flowering of male and female parent lines in hybrid production, for example. Another use is to advance or retard the flowering in accordance with the dictates of the climate so as to extend or reduce the growing season. This may involve use of anti-sense or sense regulation, discussed further below.
As noted below, other physical characteristics of plants may be affected by means of expression from nucleic acid according to the present invention.
Nucleic acid according to the invention, such as an ESD4 gene or homologue, may be placed under the control of an externally inducible gene promoter to place the timing of flowering under the control of the user. An advantage of introduction of a heterologous gene into a plant cell, particularly when the cell is comprised in a plant, is the ability to place expression of the gene under the control of a promoter of choice, in order to be able to influence gene expression, and therefore flowering, according to preference. Furthermore, mutants and derivatives of the wild-type gene, eg with higher or lower activity than wild-type, may be used in place of the endogenous gene.
In the present invention, over-expression may be achieved by introduction of the nucleotide sequence in a sense orientation. Thus, the present invention provides a method of influencing a physical e.g. flowering characteristic of a plant, the method including causing or allowing expression of the product (polypeptide or nucleic acid transcript) encoded by heterologous nucleic acid according to the invention from that nucleic acid within cells of the plant.
Down-regulation of expression of a target gene may be achieved using anti-sense technology or xe2x80x9csense regulationxe2x80x9d (xe2x80x9cco-suppressionxe2x80x9d).
In using anti-sense genes or partial gene sequences to down-regulate gene expression, a nucleotide sequence is placed under the control of a promoter in a xe2x80x9creverse orientationxe2x80x9d such that transcription yields RNA which is complementary to normal mRNA transcribed from the xe2x80x9csensexe2x80x9d strand of the target gene. See, for example, Rothstein et al, 1987; Smith et al, (1988) Nature 334, 724-726; Zhang et al,(1992) The Plant Cell 4, 1575-1588, English et al., (1996) The Plant Cell 8, 179-188. Antisense technologyis also reviewed in Bourque, (1995), Plant Science 105, 125-149, and Flavell, (1994) PNAS USA 91, 3490-3496.
An alternative is to use a copy of all or part of the target gene inserted in sense, that is the same, orientation as the target gene, to achieve reduction in expression of the target gene by co-suppression. See, for example, van der Krol et al., (1990) The Plant Cell 2, 291-299; Napoli et al., (1990) The Plant Cell 2, 279-289; Zhang et al., (1992) The Plant Cell 4, 1575-1588, and US-A-5,231,020. Further refinements of gene silencing or co-suppression technology may be found in WO95/34668 (Biosource); Angell and Baulcombe (1997) The EMBO Journal 16,12:3675-3684; and Voinnet and Baulcombe (1997) Nature 389: pg 553.
The complete sequence corresponding to the coding sequence (in reverse orientation for anti-sense) need not be used. For example fragments of sufficient length may be used. It is a routine matter for the person skilled in the art to screen fragments of various sizes and from various parts of the coding sequence to optimise the level of anti-sense inhibition. It may be advantageous to include the initiating methionine ATG codon, and perhaps one or more nucleotides upstream of the initiating codon. A further possibility is to target a conserved sequence of a gene, e.g. a sequence that is characteristic of one or more genes, such as a regulatory sequence.
The sequence employed may be about 500 nucleotides or less, possibly about 400 nucleotides, about 300 nucleotides, about 200 nucleotides, or about 100 nucleotides. It may be possible to use oligonucleotides of much shorter lengths, 14-23 nucleotides, although longer fragments, and generally even longer than about 500 nucleotides are preferable where possible, such as longer than about 600 nucleotides, than about 700 nucleotides, than about 800 nucleotides, than about 1000 nucleotides or more.
It may be preferable that there is complete sequence identity in the sequence used for down-regulation of expression of a target sequence, and the target sequence, though total complementarity or similarity of sequence is not essential. One or more nucleotides may differ in the sequence used from the target gene. Thus, a sequence employed in a down-regulation of gene expression in accordance with the present invention may be a wild-type sequence (e.g. gene) selected from those available, or a mutant, derivative, variant or allele, by way of insertion, addition, deletion or substitution of one or more nucleotides, of such a sequence. The sequence need not include an open reading frame or specify an RNA that would be translatable. It may be preferred for there to be sufficient homology for the respective anti-sense and sense RNA molecules to hybridise. There may be down regulation of gene expression even where there is about 5%, 10%, 15% or 20% or more mismatch between the sequence used and the target gene.
Generally, the transcribed nucleic acid may represent a fragment of an ESD4 gene, such as including a nucleotide sequence shown in FIG. 1 or FIG. 2, or the complement thereof, or may be a mutant, derivative, variant or allele thereof, in similar terms as discussed above in relation to alterations being made to an ESD4 coding sequence and the homology of the altered sequence. The homology may be sufficient for the transcribed anti-sense RNA to hybridise with nucleic acid within cells of the plant, though irrespective of whether hybridisation takes place the desired effect is down-regulation of gene expression.
Thus, the present invention also provides a method of influencing a flowering characteristic of a plant, the method including causing or allowing anti-sense transcription from heterologous nucleic acid according to the invention within cells of the plant.
The present invention further provides the use of the nucleotide sequence of FIG. 1 or FIG. 2 or a fragment, mutant, derivative, allele, variant or homologue thereof for down-regulation of gene expression, particularly down-regulation of expression of an ESD4 gene or homologue thereof, preferably in order to influence a physical characteristic of a plant, especially a flowering characteristic such as the timing of flowering.
When additional copies of the target gene are inserted in sense, that is the same, orientation as the target gene, a range of phenotypes is produced which includes individuals where over-expression occurs and some where under-expression of protein from the target gene occurs. When the inserted gene is only part of the endogenous gene the number of under-expressing individuals in the transgenic population increases. The mechanism by which sense regulation occurs, particularly down-regulation, is not well-understood. However, this technique is also well-reported in scientific and patent literature and is used routinely for gene control. See, for example, van der Krol et al., (1990) The Plant Cell 2, 291-229; Napoli et al., (1990) The Plant Cell 2, 279-289; Zhang et al, 1992 The Plant Cell 4, 1575-1588.
Again, fragments, mutants and so on may be used in similar terms as described above for use in anti-sense regulation.
Thus, the present invention also provides a method of influencing a flowering characteristic of a plant, the method including causing or allowing expression from nucleic acid according to the invention within cells of the plant. This may be used to suppress activity of a product with ability to influence a flowering characteristic. Here the activity of the product is preferably suppressed as a result of under-expression within the plant cells.
Reduction of gene activity may also be achieved by using ribozymes, such as replication ribozymes, e.g. of the hammerhead class (Haseloff and Gerlach, 1988, Nature 334: 585-591; Feyter et al. Mol., 1996, Gen. Genet. 250: 329-338).
Another way to reduce gene activity in a plant employs transposon mutagenesis (reviewed by Osborne et al., (1995) Current Opinion in Cell Biology 7, 406-413). Inactivation of genes has been demonstrated via a xe2x80x9ctargeted taggingxe2x80x9d approach using either endogenous mobile elements or heterologous cloned transposons which retain their mobility in alien genomes. Alleles carrying any insertion of known sequence may be identified by using PCR primers with binding specificities both in the insertion sequence and the homologue. xe2x80x9cTwo-element systemsxe2x80x9d may be used to stabilize the transposon within inactivated alleles. In the two-element approach, a T-DNA is constructed bearing a non-autonomous transposon containing selectable or screenable marker gene inserted into an excision marker. Plants bearing these T-DNAs are crossed to plants bearing a second T-DNA expressing transposase function. Hybrids aredouble-selected for excision and for the marker within the transposon yielding F2 plants with transposed elements.
Early flowering caused by reduced expression of the ESD4 gene
As described in Example 1, the esd4 mutation causes early flowering under long and short day conditions and is caused by a deletion that decreases expression of the gene. Example demonstrates that introduction of the ESD4 gene into the mutant is sufficient to correct the defect caused by the mutation. This provides indication that the function of the ESD4 gene is to repress flowering and that reduction in its function causes the plant to flower early.
Causing late flowering by increasing the activity of ESD4 The observation that reduced expression of the ESD4 gene accelerates flowering provides indication that the normal function of ESD4 is to delay flowering. Increasing the expression of the ESD4 gene is indicated for use in causing late flowering. This is supported by the observation that in wild-type plants the ESD4 mRNA is rare; it was only detected by RT-PCR and is absent from libraries of randomly sequenced cDNAs. Increasing the level of the ESD4 mRNA by expressing the gene from strong plant promoters such as the CaMV 35S promoter may be used to cause late flowering.
Aspects and embodiments of the present invention will now be illustrated, by way of example, with reference to the accompanying figures. Further aspects and embodiments will be apparent to those skilled in the art. All documents mentioned in this text are incorporated herein by reference.